{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001080","ANALYSIS_ID":"AN001763","VERSION":"1","CREATED_ON":"October 26, 2018, 7:12 pm"},

"PROJECT":{"PROJECT_TITLE":"13C Labeling Analysis of Synechococcus sp. PCC 7002","PROJECT_TYPE":"13C tracing in intracellular metabolites of PCC 7002","PROJECT_SUMMARY":"An experiment conducted for Metabolic Flux Analysis of wild-type cyanobacterium Synechococcus sp. PCC 7002","INSTITUTE":"Indian Institute of Technology Bombay (IIT Bombay)","DEPARTMENT":"Department of Chemical Engineering","LABORATORY":"Bio systems Engineering Lab","LAST_NAME":"Wangikar","FIRST_NAME":"Pramod","ADDRESS":"IIT Bombay","EMAIL":"wangikar@iitb.ac.in","PHONE":"2225767232","FUNDING_SOURCE":"Department of Biotechnology (DBT), PAN-IIT Centre for Bioenergy"},

"STUDY":{"STUDY_TITLE":"Dynamic labeling of intracellular metabolites in PCC 7002","STUDY_TYPE":"Timecourse experiment","STUDY_SUMMARY":"The experiment was conducted in a reactor at a metabolic steady state (OD 730 nm = 0.8). 13C labeled sodium bicarbonate was used as a tracer. Tracer concentration was 1 g/L. After the introduction of the tracer, the samples were collected at time point : 0, 60, 120, 180 and 240 secs. Samples were quenched with methanol and extracted using methanol-chloroform-water method. Extracts were stored at -80 degree C till LCMS analysis.","INSTITUTE":"Indian Institute of Technology, Bombay","DEPARTMENT":"Department of Chemical Engineering","LABORATORY":"Bio systems Engineering Lab","LAST_NAME":"Wangikar","FIRST_NAME":"Pramod","ADDRESS":"Powai","EMAIL":"wangikar@iit.ac.in","PHONE":"2225767232"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Synechococcus sp. PCC 7002","TAXONOMY_ID":"1131","GENOTYPE_STRAIN":"Synechococcus"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"PCC 7002 0 SEC REP 1",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 0 SEC REP 2",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 60 SEC REP 1",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 60 SEC REP 2",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 120 SEC REP 1",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 120 SEC REP 2",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 180 SEC REP 1",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 180 SEC REP 2",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 240 SEC REP 1",
"Factors":{"Genotype":"Wild type"}
},
{
"Subject ID":"-",
"Sample ID":"PCC 7002 240 SEC REP 2",
"Factors":{"Genotype":"Wild type"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The experiment was conducted in a reactor at a metabolic steady state (OD 730 nm = 0.8). 13C labeled sodium bicarbonate was used as a tracer. Tracer concentration was 1 g/L. After the introduction of the tracer, 15 mL of the culture were collected at time point : 0, 60, 120, 180 and 240 secs. Samples were quenched with methanol and extracted using methanol-chloroform-water method. Extracts were stored at -80 degree C till LCMS analysis. LCMS analysis was done in negative ion mode using information dependent aquisition (IDA) method.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"The metabolites were extracted using a methanol-chloroform-water method described in the Metabolite Extraction Protocol_PCC 7002 file of the collection data."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The metabolite extracts of different collected samples were reconstituted in 100 μL of 50/50 methanol-water mixture and filtered before injecting on LC/MS. Injection volume was 10 μL."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Shimadzu 20AD","COLUMN_NAME":"Phenomenex Synergi Hydro RP (100 x 2mm, 2.5um)","FLOW_GRADIENT":"0% B (0 min), 0% B (2min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min), 90% B (20.5 min) and 0% B (22 min)","FLOW_RATE":"0.3 mL/minute","SOLVENT_A":"10 mM tributylamine + 15mM acetic acid in water","SOLVENT_B":"100% Methanol"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"ABI Sciex 5600+ TripleTOF","INSTRUMENT_TYPE":"Triple TOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"Peak Area",

"Data":[{"Metabolite":"3-phosphoglyceric acid","PCC 7002 0 SEC REP 1":"1825000","PCC 7002 0 SEC REP 2":"1809914.748","PCC 7002 60 SEC REP 1":"397000","PCC 7002 60 SEC REP 2":"397864.7562","PCC 7002 120 SEC REP 1":"189600","PCC 7002 120 SEC REP 2":"189758.9978","PCC 7002 180 SEC REP 1":"146500","PCC 7002 180 SEC REP 2":"146531.1831","PCC 7002 240 SEC REP 1":"143800","PCC 7002 240 SEC REP 2":"144545.2416"},{"Metabolite":"Acetyl coenzyme A","PCC 7002 0 SEC REP 1":"216300","PCC 7002 0 SEC REP 2":"187144.5723","PCC 7002 60 SEC REP 1":"103000","PCC 7002 60 SEC REP 2":"95456.91977","PCC 7002 120 SEC REP 1":"37110","PCC 7002 120 SEC REP 2":"31014.91095","PCC 7002 180 SEC REP 1":"20430","PCC 7002 180 SEC REP 2":"20311.98449","PCC 7002 240 SEC REP 1":"12440","PCC 7002 240 SEC REP 2":"17766.67371"},{"Metabolite":"ADP-Glucose","PCC 7002 0 SEC REP 1":"236363.7529","PCC 7002 0 SEC REP 2":"231200","PCC 7002 60 SEC REP 1":"36776.77178","PCC 7002 60 SEC REP 2":"39160","PCC 7002 120 SEC REP 1":"3497.701153","PCC 7002 120 SEC REP 2":"15740","PCC 7002 180 SEC REP 1":"11782.81148","PCC 7002 180 SEC REP 2":"12170","PCC 7002 240 SEC REP 1":"8055.256363","PCC 7002 240 SEC REP 2":"12020"},{"Metabolite":"ADP","PCC 7002 0 SEC REP 1":"1052000","PCC 7002 0 SEC REP 2":"615952.645","PCC 7002 60 SEC REP 1":"2283000","PCC 7002 60 SEC REP 2":"1291472.518","PCC 7002 120 SEC REP 1":"1585000","PCC 7002 120 SEC REP 2":"1436972.627","PCC 7002 180 SEC REP 1":"2090000","PCC 7002 180 SEC REP 2":"1344884.102","PCC 7002 240 SEC REP 1":"1908000","PCC 7002 240 SEC REP 2":"1447495.999"},{"Metabolite":"Aspartic acid","PCC 7002 0 SEC REP 1":"166843.8049","PCC 7002 0 SEC REP 2":"169799.7716","PCC 7002 60 SEC REP 1":"46379.87345","PCC 7002 60 SEC REP 2":"46394.01629","PCC 7002 120 SEC REP 1":"29962.95559","PCC 7002 120 SEC REP 2":"30920.09425","PCC 7002 180 SEC REP 1":"21953.58061","PCC 7002 180 SEC REP 2":"25995.42161","PCC 7002 240 SEC REP 1":"27922.77487","PCC 7002 240 SEC REP 2":"25512.83817"},{"Metabolite":"ATP","PCC 7002 0 SEC REP 1":"5865000","PCC 7002 0 SEC REP 2":"2619389.732","PCC 7002 60 SEC REP 1":"6068000","PCC 7002 60 SEC REP 2":"2597088.33","PCC 7002 120 SEC REP 1":"4210000","PCC 7002 120 SEC REP 2":"4017615.333","PCC 7002 180 SEC REP 1":"4567000","PCC 7002 180 SEC REP 2":"2500348.74","PCC 7002 240 SEC REP 1":"3580000","PCC 7002 240 SEC REP 2":"2521826.67"},{"Metabolite":"Citric acid","PCC 7002 0 SEC REP 1":"16280000","PCC 7002 0 SEC REP 2":"27137352.32","PCC 7002 60 SEC REP 1":"22060000","PCC 7002 60 SEC REP 2":"28545016.49","PCC 7002 120 SEC REP 1":"21300000","PCC 7002 120 SEC REP 2":"29048720.45","PCC 7002 180 SEC REP 1":"20530000","PCC 7002 180 SEC REP 2":"28784886.33","PCC 7002 240 SEC REP 1":"32090000","PCC 7002 240 SEC REP 2":"32332715.78"},{"Metabolite":"Glucose 6 phosphate","PCC 7002 0 SEC REP 1":"372300","PCC 7002 0 SEC REP 2":"280300","PCC 7002 60 SEC REP 1":"101200","PCC 7002 60 SEC REP 2":"98670","PCC 7002 120 SEC REP 1":"53930","PCC 7002 120 SEC REP 2":"74170","PCC 7002 180 SEC REP 1":"64950","PCC 7002 180 SEC REP 2":"28140","PCC 7002 240 SEC REP 1":"912.3","PCC 7002 240 SEC REP 2":"27410"},{"Metabolite":"Glutamic acid","PCC 7002 0 SEC REP 1":"6454000","PCC 7002 0 SEC REP 2":"6120000","PCC 7002 60 SEC REP 1":"5328000","PCC 7002 60 SEC REP 2":"5517000","PCC 7002 120 SEC REP 1":"5847000","PCC 7002 120 SEC REP 2":"5393000","PCC 7002 180 SEC REP 1":"4624000","PCC 7002 180 SEC REP 2":"4460000","PCC 7002 240 SEC REP 1":"5029000","PCC 7002 240 SEC REP 2":"4782000"},{"Metabolite":"Leucine","PCC 7002 0 SEC REP 1":"187332.3245","PCC 7002 0 SEC REP 2":"190645.4362","PCC 7002 60 SEC REP 1":"194909.8116","PCC 7002 60 SEC REP 2":"184260.5519","PCC 7002 120 SEC REP 1":"138918.3898","PCC 7002 120 SEC REP 2":"143141.446","PCC 7002 180 SEC REP 1":"112073.1538","PCC 7002 180 SEC REP 2":"120720.6836","PCC 7002 240 SEC REP 1":"127840.8323","PCC 7002 240 SEC REP 2":"119246.7778"},{"Metabolite":"Malate","PCC 7002 0 SEC REP 1":"715771.8932","PCC 7002 0 SEC REP 2":"738800","PCC 7002 60 SEC REP 1":"432258.8547","PCC 7002 60 SEC REP 2":"439300","PCC 7002 120 SEC REP 1":"260719.5945","PCC 7002 120 SEC REP 2":"234500","PCC 7002 180 SEC REP 1":"146536.8448","PCC 7002 180 SEC REP 2":"153700","PCC 7002 240 SEC REP 1":"142233.436","PCC 7002 240 SEC REP 2":"158300"},{"Metabolite":"nicotinamide adenine dinucleotide","PCC 7002 0 SEC REP 1":"211900","PCC 7002 0 SEC REP 2":"197184.9309","PCC 7002 60 SEC REP 1":"224800","PCC 7002 60 SEC REP 2":"212751.8614","PCC 7002 120 SEC REP 1":"219600","PCC 7002 120 SEC REP 2":"200295.1679","PCC 7002 180 SEC REP 1":"174000","PCC 7002 180 SEC REP 2":"170269.6746","PCC 7002 240 SEC REP 1":"232700","PCC 7002 240 SEC REP 2":"232441.5314"},{"Metabolite":"Sedoheptulose 7 phosphate","PCC 7002 0 SEC REP 1":"561900","PCC 7002 0 SEC REP 2":"444300","PCC 7002 60 SEC REP 1":"95910","PCC 7002 60 SEC REP 2":"80200","PCC 7002 120 SEC REP 1":"67200","PCC 7002 120 SEC REP 2":"64530","PCC 7002 180 SEC REP 1":"48110","PCC 7002 180 SEC REP 2":"49620","PCC 7002 240 SEC REP 1":"59100","PCC 7002 240 SEC REP 2":"51200"},{"Metabolite":"Succinic acid","PCC 7002 0 SEC REP 1":"789700","PCC 7002 0 SEC REP 2":"800000","PCC 7002 60 SEC REP 1":"493700","PCC 7002 60 SEC REP 2":"498700","PCC 7002 120 SEC REP 1":"349200","PCC 7002 120 SEC REP 2":"358300","PCC 7002 180 SEC REP 1":"349400","PCC 7002 180 SEC REP 2":"354000","PCC 7002 240 SEC REP 1":"349500","PCC 7002 240 SEC REP 2":"373700"},{"Metabolite":"Sucrose","PCC 7002 0 SEC REP 1":"3470000","PCC 7002 0 SEC REP 2":"3497112.158","PCC 7002 60 SEC REP 1":"3144000","PCC 7002 60 SEC REP 2":"3251845.298","PCC 7002 120 SEC REP 1":"3246000","PCC 7002 120 SEC REP 2":"3278608.459","PCC 7002 180 SEC REP 1":"2884000","PCC 7002 180 SEC REP 2":"2906881.366","PCC 7002 240 SEC REP 1":"3229000","PCC 7002 240 SEC REP 2":"3258915.414"},{"Metabolite":"Tyrosine","PCC 7002 0 SEC REP 1":"666178.3389","PCC 7002 0 SEC REP 2":"645388.2082","PCC 7002 60 SEC REP 1":"448455.8569","PCC 7002 60 SEC REP 2":"439872.226","PCC 7002 120 SEC REP 1":"310685.8726","PCC 7002 120 SEC REP 2":"310750.3772","PCC 7002 180 SEC REP 1":"217046.6913","PCC 7002 180 SEC REP 2":"218686.6716","PCC 7002 240 SEC REP 1":"229142.4485","PCC 7002 240 SEC REP 2":"217703.2177"},{"Metabolite":"UDP-Glucose","PCC 7002 0 SEC REP 1":"199027.6441","PCC 7002 0 SEC REP 2":"171900","PCC 7002 60 SEC REP 1":"62667.22165","PCC 7002 60 SEC REP 2":"61770","PCC 7002 120 SEC REP 1":"25495.70979","PCC 7002 120 SEC REP 2":"20050","PCC 7002 180 SEC REP 1":"12722.99954","PCC 7002 180 SEC REP 2":"12060","PCC 7002 240 SEC REP 1":"7464.802252","PCC 7002 240 SEC REP 2":"3018"},{"Metabolite":"Uridine monophosphate","PCC 7002 0 SEC REP 1":"3068000","PCC 7002 0 SEC REP 2":"2565363.449","PCC 7002 60 SEC REP 1":"4767000","PCC 7002 60 SEC REP 2":"4423167.365","PCC 7002 120 SEC REP 1":"4537000","PCC 7002 120 SEC REP 2":"4324243.151","PCC 7002 180 SEC REP 1":"4025000","PCC 7002 180 SEC REP 2":"3851815.727","PCC 7002 240 SEC REP 1":"5162000","PCC 7002 240 SEC REP 2":"5089080.562"}],

"Metabolites":[{"Metabolite":"3-phosphoglyceric acid","Elemental formula":"C3H7O7P","KEGG ID":"C00197","retention index (min)":"12.29"},{"Metabolite":"Acetyl coenzyme A","Elemental formula":"C23H38N7O17P3S","KEGG ID":"C00024","retention index (min)":"15.36"},{"Metabolite":"ADP-Glucose","Elemental formula":"C16H25N5O15P2","KEGG ID":"C00498","retention index (min)":"12.54"},{"Metabolite":"ADP","Elemental formula":"C10H15N5O10P2","KEGG ID":"C00008","retention index (min)":"13.76"},{"Metabolite":"Aspartic acid","Elemental formula":"C4H7NO4","KEGG ID":"C00049","retention index (min)":"5.14"},{"Metabolite":"ATP","Elemental formula":"C10H16N5O13P3","KEGG ID":"C00002","retention index (min)":"14.93"},{"Metabolite":"Citric acid","Elemental formula":"C6H8O7","KEGG ID":"C00158","retention index (min)":"13.6"},{"Metabolite":"Glucose 6 phosphate","Elemental formula":"C6H13O9P","KEGG ID":"C00668","retention index (min)":"7.34"},{"Metabolite":"Glutamic acid","Elemental formula":"C5H9NO4","KEGG ID":"C00025","retention index (min)":"5.09"},{"Metabolite":"Leucine","Elemental formula":"C6H13NO2","KEGG ID":"C00123","retention index (min)":"2.35"},{"Metabolite":"Malate","Elemental formula":"C4H6O5","KEGG ID":"C00149","retention index (min)":"11.5"},{"Metabolite":"nicotinamide adenine dinucleotide","Elemental formula":"C21H28N7O14P2","KEGG ID":"C00003","retention index (min)":"9.86"},{"Metabolite":"Sedoheptulose 7 phosphate","Elemental formula":"C7H15O10P","KEGG ID":"C05382","retention index (min)":"7.99"},{"Metabolite":"Succinic acid","Elemental formula":"C4H6O4","KEGG ID":"C00042","retention index (min)":"11.3"},{"Metabolite":"Sucrose","Elemental formula":"C12H22O11","KEGG ID":"C00089","retention index (min)":"1.57"},{"Metabolite":"Tyrosine","Elemental formula":"C9H11NO3","KEGG ID":"C00082","retention index (min)":"3.3"},{"Metabolite":"UDP-Glucose","Elemental formula":"C15H24N2O17P2","KEGG ID":"C00029","retention index (min)":"11.46"},{"Metabolite":"Uridine monophosphate","Elemental formula":"C9H13N2O9P","KEGG ID":"C00105","retention index (min)":"10.3"}]
}

}